Remove Gene Signature
2019/04/08
1 Regress out gene signature
As we have now the gene signature for each cell type, we seek to correct for the observed bias to meet two objectives:
- Remove technical artifacts. We will visualize this as an increased ‘mixedness’ of “affected” and “unaffected” clusters.
- Preserve biological variability. Our purpose is that the only HVG that get lost are the ones present in the meta-signature.
To achieve that, we will regress out the time-score variable we computed for each cell in previous notebooks only for the genes in the meta-signatures. We will plot the tSNEs (with the HVG) before and after the correction to assess the overall performance.
This procedure is inspired by the correction of the cell cycle variability carried out in previous studies. We refer the reader to the following articles and Seurat vignette for a full understanding:
- http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=27124452
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028641/#MOESM4
- https://satijalab.org/seurat/cell_cycle_vignette.html
library(SingleCellExperiment)
library(scater)
library(scran)
library(Seurat)
library(EnsDb.Hsapiens.v86)
library(ggpubr)
library(org.Hs.eg.db)
library(biomaRt)
library(SC3)
library(pheatmap)
library(BiocStyle)
library(purrr)
library(ggrepel)
library(plotROC)
library(caret)
library(ROCR)
library(pheatmap)
library(org.Hs.eg.db)
library(GOstats)
library(VennDiagram)
library(ggplotify)
library(scales)
library(ggridges)
library(tidyverse)
source("bin/utils.R")
# Load SingleCellExperiment object
sce_10x <- readRDS("results/R_objects/sce_10x_scored.rds")
# Load list with metasignatures
metasignatures <- readRDS("results/R_objects/metasignatures.rds")
# Plot PCA all cells colored by label ("affected" or "unaffected")
cell_types <- c("CD4 T", "CD8 T", "NK", "Monocyte", "B")
seurat_10x <- Convert(from = sce_10x, to = "seurat")
seurat_10x <- SetAllIdent(seurat_10x, id = "cell_type")
seurat_list <- list(
"CD4 T" = list(),
"CD8 T" = list(),
"NK" = list(),
"Monocyte" = list(),
"B" = list()
)
tsne_list <- seurat_list
for (cell_type in cell_types) {
seurat_sub <- SubsetData(seurat_10x, ident.use = cell_type)
for (i in c("not regressed", "regressed")) {
seurat_curr <- ScaleData(seurat_sub, display.progress = FALSE)
if (i == "regressed") {
scaled_data_all <- seurat_curr@scale.data
seurat_curr <- ScaleData(
seurat_curr,
genes.use = metasignatures[[cell_type]],
vars.to.regress = "time_score",
display.progress = FALSE
)
scaled_data_all[rownames(seurat_curr@scale.data), ] <- seurat_curr@scale.data
seurat_curr@scale.data <- scaled_data_all
}
seurat_curr <- FindVariableGenes(
seurat_curr,
do.plot = FALSE,
display.progress = FALSE,
binning.method = "equal_frequency"
)
seurat_curr <- SetAllIdent(seurat_curr, id = "label")
seurat_curr <- RunPCA(
seurat_curr,
pc.genes = seurat_curr@var.genes
)
seurat_curr <- RunTSNE(seurat_curr)
tsne_list[[cell_type]][[i]] <- TSNEPlot(seurat_curr)
seurat_list[[cell_type]][[i]] <- seurat_curr
}
}## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "RPS6" "RPL32" "RPS12" "RPS3A" "RPL21" "RPLP2" "RPL13" "RPL9" "RPS14" "RPL31" "RPS15A" "RPS23" "RPS13" "RPS27A" "RPL34" "RPL39" "RPS25" "RPS8" "RPL30" "RPL11" "RPL35A" "RPS28" "RPS27" "RPL19" "RPL7" "RPL10" "RPL3" "RPS16" "RPL18A" "RPL13A"
## [1] ""
## [1] "B2M" "S100A4" "ACTB" "TMSB4X" "IL32" "HLA-A" "CD52" "MT-CO1" "HLA-B" "ANXA2" "CRIP1" "GZMA" "GZMK" "LTB" "JUNB" "TMSB10" "LINC00152" "CCL5" "HLA-DPA1" "HOPX" "HLA-DPB1" "KLRB1" "UCP2" "LPAR6" "LGALS3" "CST7" "TNFSF10" "PRDM1" "MT-CO2" "ISG15"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "FTH1" "EIF1" "RPS29" "H3F3B" "MALAT1" "CREM" "EZR" "ZNF331" "RPS27" "GABARAPL1" "HERPUD1" "BTG3" "PMAIP1" "RP11-51J9.5" "PIK3R1" "ZFP36" "H1FX" "SYTL3" "TSPYL2" "FAM177A1" "REL" "EEF1A1" "RGS1" "YWHAH" "JUND" "DUSP2" "RGS2" "SLC2A3" "RPL3" "RBPJ"
## [1] ""
## [1] "TMSB10" "CD52" "TMSB4X" "IL32" "B2M" "ACTB" "LTB" "RPL41" "MT-CO1" "RPS12" "MT-ND4" "RPS8" "S100A4" "UCP2" "RPS3A" "RPS25" "RPL13" "MT-ATP6" "RPLP2" "RPL19" "MT-CYB" "RPL32" "MT-CO2" "RPL28" "RPS14" "C1orf162" "RPS23" "RPS26" "RPL11" "RPLP1"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "MALAT1" "XIST" "RPS29" "RPS27" "MT-CO3" "MT-CO1" "RPS4X" "RPL34" "TMSB10" "RPL21" "MT-ND3" "RPL7" "RPS18" "TMSB4X" "LDLRAP1" "NUCB2" "AIF1" "STMN1" "RPL3" "RPL31" "RPL39" "MT-ND4" "HLA-B" "FAIM3" "RPS28" "MT-CYB" "ID3" "TAGAP" "ANKRD44" "RPS14"
## [1] ""
## [1] "RPS26" "KLRB1" "RPL28" "RPS16" "RPLP1" "FTH1" "RPS12" "RPL10" "GNLY" "IL32" "S100A4" "CREM" "RPS19" "TNFRSF4" "RPL13A" "FAM177A1" "LGALS3" "RPS8" "JUNB" "EIF1" "RPL27A" "HOPX" "RPL18A" "ATG2A" "ANXA2" "RPL13" "ZNF331" "B4GALT1" "PIK3R1" "CNOT6L"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "MT-ND2" "MT-CYB" "MT-CO2" "MT-ND4" "MT-ATP6" "CCL5" "MT-CO3" "MT-ND3" "GZMK" "MT-CO1" "NKG7" "RPL27A" "GZMA" "CST7" "RPS19" "CD8B" "FTH1" "DUSP2" "GNLY" "RPL23A" "RPL41" "CD8A" "RPL13A" "RPS27A" "RPLP2" "B2M" "RPL34" "RPS16" "RPLP1" "RPS3"
## [1] ""
## [1] "TSHZ2" "TMSB10" "IL6ST" "ID3" "FHIT" "C1orf162" "STMN1" "MARCKSL1" "LTB" "LPAR6" "CD52" "UCP2" "PIM2" "HLA-DRA" "FAIM3" "LDLRAP1" "RPS13" "RP11-51J9.5" "BIRC3" "LIMS1" "H1FX" "ACTB" "ISG15" "YIPF4" "XIST" "MAPKAPK5-AS1" "FXR1" "RBCK1" "KAT6A" "OTUB1"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "MT-ATP6" "RPS26" "CD8B" "MT-CO2" "MT-ND2" "AIF1" "MT-ND4" "MT-CYB" "CD8A" "FHIT" "MALAT1" "MT-ND3" "HLA-DPB1" "APBA2" "MT-CO3" "RGS1" "CMC1" "NKG7" "RPLP2" "ANKRD44" "OGT" "RPL28" "NUCB2" "RPS16" "CCL5" "JUND" "HLA-DPA1" "TTC14" "MDM4" "CST7"
## [1] ""
## [1] "LTB" "RPS4X" "KLRB1" "EEF1A1" "RPS18" "S100A4" "RPL3" "RPS2" "RPL10" "JUNB" "RPL41" "TNFRSF4" "HLA-B" "B2M" "CRIP1" "RPL18A" "RPL34" "HOPX" "RPL39" "ANXA2" "HLA-A" "ACTB" "CD52" "RPL21" "RPL23A" "RPS29" "RPS3" "RPL13A" "LGALS3" "FTH1"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "RPL32" "RPS3A" "RPS12" "RPS6" "RPL13" "RPLP2" "RPS14" "RPS23" "RPL21" "RPS15A" "RPS13" "RPL31" "RPS27A" "RPS8" "RPS25" "RPL19" "RPL11" "RPL34" "RPL35A" "RPL30" "RPL9" "RPS28" "RPL10" "RPL7" "RPL18A" "RPL13A" "RPL39" "RPLP1" "RPL27A" "RPS19"
## [1] ""
## [1] "FTH1" "HLA-B" "S100A4" "HLA-A" "EIF1" "ANXA2" "B2M" "JUNB" "LINC00152" "GZMK" "CCL5" "CREM" "EZR" "KLRB1" "HLA-DPA1" "HLA-DPB1" "ACTB" "HOPX" "GZMA" "CST7" "H3F3B" "LGALS3" "IL32" "HERPUD1" "PRDM1" "PIK3R1" "CRIP1" "GATA3" "RGS1" "NKG7"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "MALAT1" "RPS29" "RPS27" "XIST" "RPS4X" "MT-CO3" "RPL34" "RPL21" "MT-CO1" "RPS18" "RPL3" "RPL7" "RPL39" "H3F3B" "MT-ND3" "ID3" "H1FX" "HLA-B" "RPL31" "RPS28" "LDLRAP1" "NUCB2" "EEF1A1" "STMN1" "AIF1" "FAIM3" "TMSB4X" "KTN1" "TAGAP" "TMSB10"
## [1] ""
## [1] "RPS26" "IL32" "RPL28" "KLRB1" "RPS16" "RPLP1" "S100A4" "RPS12" "GNLY" "RPL10" "RPS19" "TNFRSF4" "RPS8" "RPL13A" "RPL27A" "CD52" "RPL13" "GZMA" "LGALS3" "HOPX" "CREM" "RPL19" "MT-ND2" "RPL18A" "ANXA2" "FTH1" "RPL41" "RPS15" "FAM177A1" "JUNB"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "TSHZ2" "FHIT" "IL6ST" "STMN1" "C1orf162" "ID3" "MARCKSL1" "TMSB10" "HLA-DRA" "PIM2" "ISG15" "UCP2" "RP11-51J9.5" "FAIM3" "LDLRAP1" "LIMS1" "LTB" "YIPF4" "LPAR6" "CD52" "BIRC3" "RBCK1" "FXR1" "MAPKAPK5-AS1" "RPS13" "KAT6A" "OTUB1" "OXNAD1" "STAT1" "H1FX"
## [1] ""
## [1] "MT-ND2" "MT-CYB" "MT-ND4" "MT-CO2" "MT-CO3" "MT-ATP6" "CCL5" "MT-CO1" "MT-ND3" "B2M" "GZMK" "RPL27A" "GZMA" "RPL41" "NKG7" "RPL34" "RPS19" "FTH1" "CST7" "RPS27A" "RPL23A" "DUSP2" "CD8B" "RPS15A" "RPL13A" "HLA-A" "IL32" "RPLP2" "RPL10" "RPS3"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "EEF1A1" "FTH1" "RPL3" "KLRB1" "RPS4X" "S100A4" "RPS2" "RPL10" "RPS18" "LTB" "EIF1" "JUNB" "RPS29" "RPL21" "RPL34" "ZFP36" "BTG3" "HERPUD1" "YWHAH" "TNFRSF4" "RPL18A" "HLA-A" "CRIP1" "RPS27" "CREM" "SYTL3" "H3F3B" "SLC2A3" "RPL39" "REL"
## [1] ""
## [1] "MT-ATP6" "MT-CO2" "MT-CYB" "MT-ND4" "MT-ND2" "CD8B" "TMSB10" "AIF1" "MT-ND3" "MT-CO1" "FHIT" "ANKRD44" "RPS26" "STMN1" "TTC14" "MT-CO3" "NUCB2" "FAIM3" "IFI6" "HLA-DPB1" "CD8A" "MTRNR2L8" "LDLRAP1" "OXNAD1" "OGT" "GPR155" "GZMK" "HLA-DPA1" "ASCC2" "MIR142"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "TMSB10" "B2M" "TMSB4X" "PTMA" "H3F3B" "ACTB" "RPS15A" "SESN3" "RGS1" "AP3M2" "FTH1" "CD52" "LPAR6" "NR3C1" "RPL41" "FAM177A1" "RPL11" "BIRC3" "MT-ATP6" "MT-CYB" "EIF1" "MT-ND4" "SLC2A3" "RPL28" "MT-CO2" "RP11-51J9.5" "JUND" "DNAJB1" "PIK3R1" "RP11-138A9.2"
## [1] ""
## [1] "GZMK" "CCL5" "NKG7" "GZMA" "GNLY" "HOPX" "CST7" "RPS2" "CD8A" "RPS29" "CMC1" "AC092580.4" "CD8B" "RPL3" "EEF1A1" "KLRB1" "DUSP2" "LGALS3" "CASP1" "EHD1" "NUCB2" "RPS19" "RPS4X" "RPS18" "RPS27" "RPL31" "HLA-B" "PSMA5" "MT-ND3" "RPS3"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "B2M" "PFN1" "ACTB" "TMSB4X" "IL32" "CD52" "TMSB10" "S100A4" "MT-CO1" "NKG7" "GZMH" "CCL5" "HLA-A" "GZMK" "HLA-C" "FAM65B" "CD8B" "HLA-DRB1" "HOPX" "SELL" "KLRF1" "LGALS1" "CMC1" "COTL1" "HLA-DRA" "FERMT3" "DDX17" "FCGR3A" "STMN1" "MT1E"
## [1] ""
## [1] "FTH1" "EIF1" "RPL10" "RPL34" "RPL21" "EEF1A1" "RPS27" "H3F3B" "TSPYL2" "RPS12" "RPS6" "RPL32" "RPL39" "FOS" "RPS27A" "JUN" "RP11-277L2.4" "JUND" "PTMA" "PMAIP1" "RPS29" "CNOT1" "RPL7" "KLRB1" "SKIL" "H1FX" "RGCC" "RPS2" "SYTL3" "RPS19"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "MALAT1" "H3F3B" "HLA-B" "NEAT1" "HLA-C" "EIF1" "MT-CO3" "H1FX" "CLK1" "PTPN7" "NKG7" "HLA-A" "CNOT1" "ZNF281" "ZEB2" "CCNH" "SPON2" "SAMSN1" "ZBTB7A" "DDIT3" "MT-CO2" "RASA2" "PICALM" "SP140L" "LAMTOR3" "SMG1" "BBC3" "HAUS3" "GMFB" "ARMCX3"
## [1] ""
## [1] "RPL13" "RPS12" "RPL32" "LTB" "RPS6" "RPL10" "RPS18" "IL32" "CD52" "RPS14" "RPS2" "RPL13A" "GZMK" "RPLP1" "RPL21" "RPS27A" "S100A4" "EEF1A1" "KLRB1" "RPS19" "RPL41" "AQP3" "RPLP2" "RPL7" "RPL34" "ACTB" "RPL39" "LST1" "LGALS3" "RPS15A"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "GNLY" "TYROBP" "NKG7" "MT-CO2" "SPON2" "KLRF1" "MT-ND4" "MT-ATP6" "FCER1G" "KLRB1" "C20orf24" "PTGDS" "MT-ND2" "CLIC3" "RPL10" "THEMIS2" "FCGR3A" "SYTL3" "RPLP1" "IFNGR1" "NEIL1" "MT-CYB" "F2R" "KLRC1" "RIN3" "C1orf162" "CCL3" "YES1" "MT-ND3" "GZMH"
## [1] ""
## [1] "XIST" "GPR183" "GZMK" "COTL1" "LTB" "RGS1" "CD52" "JUN" "SAMSN1" "HLA-DRB1" "RPS29" "RPS18" "ASF1A" "RPL39" "IL32" "RPS27" "PLK3" "H1FX" "NABP1" "ACTB" "ARMCX3" "TMBIM6" "GPR82" "HSPB1" "RPS2" "SMARCC1" "NIN" "NFKBIZ" "CD8B" "CCDC66"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "KLRB1" "GNLY" "TYROBP" "MT-ND2" "ACAA2" "MT-ND4" "MT-CO2" "MT-CYB" "MT-ATP6" "ARHGAP5" "S100A4" "FCER1G" "PDE7A" "KLRF1" "RP11-83A24.2" "NAA16" "S100A9" "TATDN1" "ADSS" "C1orf162" "NXT1" "FNTA" "HOPX" "PTMA" "BMS1" "CERS5" "GPR82" "RASA2" "DMTF1" "C15orf61"
## [1] ""
## [1] "RPS29" "HLA-DRB1" "MALAT1" "RPS27" "CD8A" "CD8B" "CCL5" "COTL1" "RPL13A" "RPS18" "HLA-B" "GZMH" "ZEB2" "HLA-DRA" "RANBP2" "SPPL2A" "PSMA6" "CENPC" "ARL6IP1" "TIPARP" "KIAA1551" "HLA-C" "MED15" "RAB8B" "CLIP1" "CMC1" "NELFE" "RFC1" "PRPF18" "ERICH1"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "RPS27" "MALAT1" "NKG7" "CMC1" "CCL5" "RPL21" "GZMH" "RPS29" "RPS14" "RPS27A" "RPS19" "RPL39" "RPS15A" "CD8B" "RPL41" "RPL13A" "HLA-B" "TMSB4X" "CEP78" "HLA-DRB1" "RPLP2" "HLA-C" "EOMES" "CD8A" "RPL7" "CCL3" "GNPTAB" "F2R" "B2M" "HLA-A"
## [1] ""
## [1] "KLRB1" "LTB" "AQP3" "BCL7C" "H2AFX" "PTMA" "USP36" "S100A4" "PRKDC" "DBF4" "RNF138" "RAB8B" "UBE2D1" "TIPARP" "RP11-356I2.4" "NELFE" "DENR" "RANBP2" "IL4R" "PTBP3" "IQGAP2" "ZNF224" "MYO9B" "RFC1" "KXD1" "SIRT2" "RPL7L1" "PRPF18" "LMAN1" "CMIP"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "MALAT1" "NKG7" "HLA-C" "B2M" "HLA-A" "HLA-B" "GZMH" "MT-CO1" "H3F3B" "MT-CO2" "TMSB10" "SPON2" "TMSB4X" "LGALS1" "TYROBP" "PFN1" "KLRF1" "GNLY" "MT-ATP6" "ZEB2" "NEAT1" "HLA-DRB1" "MT-CO3" "PTPN7" "ZBTB7A" "FCER1G" "FCGR3A" "C20orf24" "CMC1" "RP11-139H15.1"
## [1] ""
## [1] "RPL13" "RPS12" "RPL32" "RPL10" "RPS6" "RPL21" "LTB" "EEF1A1" "RPS2" "RPS18" "RPL13A" "RPS14" "RPS27A" "RPLP1" "KLRB1" "RPL34" "RPS19" "GZMK" "RPL7" "RPLP2" "RPL39" "AQP3" "RPL41" "IL32" "CD52" "RPS15A" "S100A4" "LST1" "RPS27" "FOS"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "JUN" "RPS27" "H1FX" "RPS29" "XIST" "RGS1" "SAMSN1" "RP11-277L2.4" "PLK3" "RPL39" "GPR183" "CD69" "RPL34" "ARMCX3" "GCC2" "LTB" "FOS" "BTG2" "NFKBIZ" "RGCC" "CLK1" "NXT1" "SKIL" "LMNA" "H3F3B" "GZMK" "HAUS3" "DNAJB1" "ASF1A" "CCNH"
## [1] ""
## [1] "GNLY" "NKG7" "TYROBP" "KLRF1" "MT-CO2" "GZMH" "B2M" "SPON2" "MT-ND4" "FCER1G" "FCGR3A" "C20orf24" "MT-ATP6" "PTGDS" "C1orf162" "RPL10" "LAIR2" "CLIC3" "CMC1" "KLRC1" "MT-CYB" "HLA-A" "KLRB1" "HLA-C" "THEMIS2" "RPLP1" "LGALS1" "S100A4" "TXK" "F2R"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "HLA-DRB1" "COTL1" "GZMH" "HLA-DRA" "CD8A" "STMN1" "CD8B" "LGALS1" "TMSB10" "CMC1" "MT1E" "ACTB" "TMSB4X" "CCL5" "PCNA" "RGS1" "XIST" "TUBB" "HLA-A" "ITGAL" "CXCR3" "MYO1G" "GPR183" "DDX17" "CD52" "IFI16" "HIST1H4C" "PAG1" "EIF1" "FKBP3"
## [1] ""
## [1] "MT-ND2" "KLRB1" "MT-CO2" "MT-ND4" "MT-CO3" "MT-ND3" "MT-ATP6" "MT-CYB" "RPL34" "GNLY" "TYROBP" "EEF1A1" "MT-CO1" "RPL7" "RPL21" "RPS6" "CD69" "RPS27A" "RPLP2" "HOPX" "RPLP1" "FCER1G" "RPL32" "RP11-277L2.4" "ARHGAP5" "IL4R" "YES1" "CXXC5" "MALAT1" "RPS12"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "KLRB1" "LTB" "PTMA" "S100A4" "AQP3" "STMN1" "IL32" "FTH1" "ACTB" "TUBB" "H2AFX" "PRKDC" "HIST1H4C" "BCL7C" "USP36" "LGALS3" "NELFE" "RAB8B" "RNF138" "IFNGR1" "UBE2D1" "DENR" "IL4R" "IQGAP2" "RANBP2" "PCNA" "DBF4" "MYO9B" "RFC1" "PRPF18"
## [1] ""
## [1] "RPS27" "MALAT1" "RPS29" "RPL21" "CCL5" "RPS14" "CMC1" "NKG7" "RPS27A" "RPL13A" "RPL39" "CD8B" "RPS15A" "RPL7" "GZMH" "RPS19" "RPL41" "HLA-B" "RPL34" "TMSB4X" "RPLP2" "EOMES" "B2M" "CD8A" "HLA-C" "CCL3" "CEP78" "GNPTAB" "NEAT1" "F2R"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "GNLY" "TYROBP" "ACAA2" "KLRF1" "KLRB1" "PDE7A" "FCER1G" "S100A9" "ARHGAP5" "C1orf162" "TATDN1" "TUBB" "CERS5" "COMMD7" "NOP56" "RASA2" "RP11-139H15.1" "S100A4" "FNTA" "C15orf61" "SMARCC1" "RP11-83A24.2" "HSPB1" "ADSS" "NLRP1" "USP22" "USF2" "NAA16" "DMTF1" "PTGDS"
## [1] ""
## [1] "RPS29" "MALAT1" "RPS18" "TIPARP" "RPS27" "CENPC" "SPPL2A" "RANBP2" "RP11-356I2.4" "PSMA6" "RAB8B" "DBF4" "PTBP3" "SH2D2A" "RFC1" "SIRT7" "COPA" "AKAP9" "TOPORS" "BCL7C" "RPL13A" "CMIP" "ZNF224" "H2AFX" "CLIP1" "YES1" "VPS37B" "RAB7L1" "PRPF18" "LMAN1"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "PFN1" "ACTB" "TMSB4X" "GZMA" "TMSB10" "B2M" "S100A4" "FCER1G" "NKG7" "GZMB" "IL32" "CD52" "CCL4" "MT-CO1" "FCRL6" "HLA-A" "CD320" "CSK" "DUT" "TUBA1B" "MYOM2" "LAIR2" "C17orf62" "MRPL34" "CCL5" "BATF" "BOLA3" "RASSF7" "DCK" "CD3D"
## [1] ""
## [1] "FTH1" "EIF1" "H3F3B" "IFNGR1" "PIK3R1" "CNOT1" "RPS27" "PMAIP1" "SLA2" "GABARAPL1" "TSPYL2" "CREM" "RPL13A" "RGS1" "JUN" "EEF1A1" "FAM177A1" "ZNF331" "RPL21" "NR4A2" "MALAT1" "OSER1" "RP11-51J9.5" "JUND" "FOS" "FAM133B" "METRNL" "EML4" "RPL10" "RPS15A"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "CD3D" "CD3G" "CD52" "RPS12" "CD8B" "RPL13A" "RPS27" "RPS19" "IL32" "RPS14" "RPLP2" "RPS15A" "CCL5" "GZMK" "CD8A" "RPL10" "RPL34" "RPL41" "RPL21" "RPS18" "RPS27A" "EEF1A1" "MT1E" "RPLP1" "LTB" "RPL7" "KLRC1" "DDX3Y" "XCL1" "SELL"
## [1] ""
## [1] "MT-CO1" "MALAT1" "FCER1G" "MT-CO3" "GZMB" "H3F3B" "MT-CO2" "HLA-C" "HLA-B" "B2M" "NKG7" "KLRB1" "MT-ND4" "PTMA" "GNLY" "HLA-A" "XIST" "MT-ATP6" "ACTB" "CCL4" "PFN1" "EIF1" "CCL3" "TMSB10" "TUBA1B" "MT-ND3" "DIP2A" "TMSB4X" "GZMA" "AK5"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "EIF1" "NKG7" "H3F3B" "KLRB1" "FOS" "RPL10" "GZMB" "NR4A2" "IRF8" "PTMA" "RGS1" "DUSP1" "FCER1G" "PMAIP1" "TSPYL2" "RGS2" "JUND" "DDIT3" "CCL4" "METRNL" "ZNF331" "JUN" "DUSP10" "CREM" "PDE4D" "RAMP1" "HIST1H1C" "SCLT1" "KRT86" "FTH1"
## [1] ""
## [1] "AP1G1" "USP7" "GPM6B" "ANKRD13D" "CNTRL" "TTTY15" "LPGAT1" "SPTAN1" "AC084018.1" "SUZ12" "CEP95" "KLF10" "LRBA" "RB1" "PSTPIP2" "CASP3" "TP53" "GDI1" "FAM78A" "FAM228B" "VAV1" "ZFC3H1" "RAD51C" "CTD-3184A7.4" "ACAT2" "DNAJC5" "ACYP2" "PIKFYVE" "CRLF3" "IKBKG"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "MT-CO2" "MT-ND2" "MT-ATP6" "MT-ND4" "GNLY" "MT-CYB" "RPL10" "RPLP2" "RPL41" "KLRB1" "RPLP1" "RPL21" "RPS12" "RPS27A" "MT-CO3" "RPS15A" "RPS14" "MT-CO1" "B2M" "RPL34" "MYOM2" "PTGDS" "MT-ND3" "EEF1A1" "RPL13A" "RPL7" "RPS19" "KLRC1" "NKG7" "PTMA"
## [1] ""
## [1] "IFNG" "JUN" "RGS1" "CD3D" "PMAIP1" "CCL3" "FOS" "CD8A" "DUSP10" "CD8B" "CD3G" "XIST" "KLF6" "CNOT1" "DUSP1" "RPS29" "H1FX" "PPP1R15A" "IRF8" "CCL4" "TUBB" "HIST1H1C" "PCNA" "LMO4" "RP11-51J9.5" "AASDHPPT" "JUND" "BTG3" "DDIT3" "STMN1"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "KLRB1" "RPLP1" "PLEKHA2" "MYOM2" "TTTY15" "AC132872.2" "STMN1" "TP53" "KLF10" "VIPR2" "KRT86" "PTMA" "FCER1G" "GON4L" "AASDHPPT" "KLRC1" "LAIR2" "RP3-477O4.14" "DDX3Y" "GZMB" "PTGDS" "DNAJC5" "NIPA2" "CASP3" "RB1" "AUTS2" "FAM177A1" "B3GNT7" "IFITM3" "DENND3"
## [1] ""
## [1] "RPS27" "RPS29" "MALAT1" "CD3D" "CD3G" "HLA-B" "HLA-C" "XIST" "RPL34" "B2M" "RPL41" "MT-CO1" "CD8B" "KLF6" "MT-CO3" "RPL21" "CD8A" "CD52" "RPS18" "RPS14" "RPL13A" "MITD1" "RPL7" "RPS27A" "EEF1A1" "TMSB4X" "CCL5" "GZMK" "MT-ND3" "RPS15A"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "CD3D" "CD52" "CD3G" "CD8B" "IL32" "RPS12" "CCL5" "RPS19" "CD8A" "GZMK" "RPLP2" "RPL13A" "RPS14" "RPS27" "RPL10" "RPS15A" "RPL41" "MT1E" "RPS18" "RPL34" "KLRC1" "LTB" "RPL21" "CD320" "S100A4" "SELL" "RPS27A" "RPLP1" "EEF1A1" "DDX3Y"
## [1] ""
## [1] "MALAT1" "H3F3B" "MT-CO3" "FCER1G" "MT-CO1" "MT-CO2" "GZMB" "HLA-B" "KLRB1" "FTH1" "EIF1" "PTMA" "HLA-C" "B2M" "MT-ND4" "NKG7" "MT-ATP6" "CCL3" "GNLY" "XIST" "DUSP1" "IRF8" "CCL4" "PMAIP1" "HLA-A" "TSPYL2" "CREM" "MT-ND3" "ACTB" "METRNL"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "TUBA1B" "GZMB" "ACTB" "STMN1" "PCNA" "DUT" "MT-CO1" "HLA-C" "XIST" "HLA-A" "MYOM2" "FCER1G" "NKG7" "MRPL34" "CSK" "TMSB10" "BOLA3" "PFN1" "ACADM" "AK5" "MRPL27" "CXCR2" "SIGLEC7" "RASSF7" "MCM7" "ANKRD36C" "GZMA" "TRPV2" "BATF" "PYCR2"
## [1] ""
## [1] "RPS27" "RPL21" "RPL13A" "RPL34" "RPS15A" "RPS14" "RPS27A" "EEF1A1" "RPS12" "RPL7" "RPL41" "RPLP2" "RP11-51J9.5" "RPS19" "EML4" "RPS29" "RPLP1" "RPS18" "MT-ND2" "NUP54" "BIRC2" "DENND3" "PSME4" "MED23" "GPM6B" "PER1" "RP11-138A9.2" "C9orf89" "PTAR1" "CEP95"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "FAM78A" "KLF10" "CNTRL" "VAV1" "IKBKG" "ACAT2" "TP53" "CRLF3" "EHMT1" "RAD51C" "RB1" "PSTPIP2" "AC084018.1" "TTTY15" "NIPA2" "LPGAT1" "AP1G1" "SUZ12" "USP7" "SPTAN1" "TUBB" "FAM228B" "CASP3" "ANKRD13D" "DNAJC5" "GTF2I" "FAM134C" "GPM6B" "PIKFYVE" "LRBA"
## [1] ""
## [1] "RPL10" "NKG7" "KLRB1" "RPL13A" "RPL41" "EEF1A1" "EIF1" "RPS15A" "FOS" "RPLP1" "RGS2" "JUND" "TMSB10" "RPL21" "KRT86" "GNLY" "RPL34" "PDE4D" "DUSP1" "IRF8" "DDIT3" "B2M" "RPS12" "DUSP10" "PER1" "GZMB" "PTMA" "BTG3" "B3GNT7" "DNAJB1"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "JUN" "PMAIP1" "RGS1" "IFNG" "FOS" "CCL3" "DUSP10" "DUSP1" "KLF6" "PPP1R15A" "IRF8" "JUND" "HIST1H1C" "H1FX" "RPS29" "CD3D" "BTG3" "DDIT3" "XIST" "H3F3B" "CD8A" "PHF1" "CCL4" "CD8B" "CNOT1" "CD3G" "SKIL" "LYST" "RP11-277L2.4" "PIK3R1"
## [1] ""
## [1] "MT-CO2" "MT-ND4" "MT-ND2" "MT-ATP6" "MT-CYB" "GNLY" "B2M" "MT-CO1" "RPLP2" "MYOM2" "MT-CO3" "KLRB1" "RPLP1" "RPL10" "RPL41" "RPS12" "TMSB10" "MT-ND3" "RPS27A" "PTGDS" "IL32" "RPL21" "S100A4" "RPS15A" "RPS14" "NKG7" "RPS19" "RPL34" "KLRC1" "TMSB4X"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "CD3D" "MALAT1" "CD3G" "B2M" "HLA-C" "RPS27" "RPS29" "HLA-B" "CD8B" "XIST" "MT-CO1" "CD8A" "CD52" "MT-CO3" "PFN1" "HLA-A" "TMSB4X" "MITD1" "RPL34" "CCL5" "RPL41" "ACTB" "AK5" "MT-ND3" "KLF6" "DNM1L" "SYNGR1" "FTX" "BCL2L13" "RPS18"
## [1] ""
## [1] "KLRB1" "FCER1G" "RPLP1" "PLEKHA2" "AC132872.2" "KLRC1" "TTTY15" "GZMB" "VIPR2" "MYOM2" "XCL1" "DDX3Y" "TP53" "IFITM3" "AASDHPPT" "KRT86" "GON4L" "CASP3" "KLF10" "SP140L" "B3GNT7" "BTG3" "CCL3" "COMMD5" "AUTS2" "RP3-477O4.14" "HAVCR2" "SOX4" "MEX3C" "PDE4D"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "PPBP" "HIST1H2AC" "PF4" "CCL5" "SDPR" "NRGN" "RGS18" "GNG11" "TUBB1" "CLU" "ACRBP" "F13A1" "RUFY1" "MMD" "NCOA4" "CCND3" "NGFRAP1" "VCL" "MAX" "YWHAH" "TLN1" "LIMS1" "TSC22D1" "MAP3K7CL" "VIM-AS1" "ETFA" "XPNPEP1" "RAP1B" "MYL12A" "RNF11"
## [1] ""
## [1] "RPL34" "RPLP1" "G0S2" "IL8" "MALAT1" "NEAT1" "C15orf48" "THBS1" "PLIN2" "FTH1" "SDC2" "CXCL2" "S100A6" "SRGN" "EREG" "LYZ" "CTA-29F11.1" "GAPDH" "PHLDA1" "HK2" "TIMP1" "ADM" "CXCL3" "ERO1L" "PTGES" "HLA-DRA" "H1F0" "EGR1" "ASPH" "SNAPC1"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "S100A4" "AIF1" "ACTB" "OAZ1" "RPS19" "TMSB4X" "DYNLL1" "ARL6IP5" "MT-CO2" "S100A9" "MYL12A" "NKG7" "GZMA" "S100A8" "HOPX" "CD74" "ISG15" "MYL6" "GNLY" "KLRB1" "GZMB" "SPON2" "CST7" "MT-CO1" "IL32" "CD7" "LYPD2" "CMC1" "SKAP2" "PRF1"
## [1] ""
## [1] "FTH1" "TIMP1" "SRGN" "G0S2" "IL8" "C15orf48" "PLIN2" "THBS1" "SAT1" "GAPDH" "SDC2" "RGCC" "HK2" "CXCL2" "CTA-29F11.1" "CD9" "PHLDA1" "SMOX" "H3F3B" "NEAT1" "GPX1" "ADM" "EREG" "CXCL3" "ERO1L" "MIR4435-1HG" "ASPH" "PTGES" "HILPDA" "MPP1"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "LYZ" "S100A9" "HLA-DRB1" "GPX1" "FCER1A" "S100A8" "CD74" "HLA-DRA" "PLBD1" "RP11-1143G9.4" "CLEC10A" "MFSD1" "S100A12" "RGS18" "S100A6" "S100A4" "YWHAH" "SDPR" "TUBA1C" "GSN" "GNG11" "PF4" "F13A1" "CAPN2" "TUBB1" "SPINT2" "MAP3K7CL" "AIF1" "SNAP23" "TMEM55A"
## [1] ""
## [1] "NKG7" "GNLY" "GZMB" "GZMA" "KLRB1" "FGFBP2" "CST7" "CD7" "HOPX" "SPON2" "PRF1" "CCL4" "IL32" "CMC1" "CCL5" "MALAT1" "B2M" "JAK1" "NEAT1" "H3F3B" "CCL3" "MAP3K8" "SAT1" "FTH1" "MT-CO2" "MT-CO3" "PLIN2" "MT-CO1" "RPS19" "C15orf48"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "HLA-DPB1" "RPS19" "NAP1L1" "CD74" "HLA-DRB1" "HLA-DRA" "LYPD2" "C1QA" "VMO1" "FTH1" "MALAT1" "SAT1" "RAP1B" "FAM110A" "MT2A" "AIF1" "BIN2" "CLEC10A" "TIMP1" "FCER1A" "CD47" "ICAM2" "NDUFA6" "CTSL" "MYL6" "ARL6IP5" "NDNL2" "SNAP23" "SNN" "SPINT2"
## [1] ""
## [1] "S100A8" "S100A9" "S100A12" "LYZ" "RP11-1143G9.4" "GPX1" "S100A6" "RPLP1" "RETN" "CSF3R" "PLBD1" "PPBP" "TMEM91" "MT-CO3" "F13A1" "S100P" "CYP1B1" "GNLY" "HOPX" "GNG11" "RPL34" "CCL5" "NRGN" "GZMA" "EGR1" "S100A4" "MT-CO1" "PF4" "RNU12" "GZMB"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "FTL" "B2M" "AIF1" "S100A4" "S100A6" "TMSB4X" "OAZ1" "SAT1" "NEAT1" "MT-CO1" "MALAT1" "ITM2B" "MT-CO2" "ACTB" "LYPD2" "FTH1" "SH3BGRL3" "H3F3B" "MT2A" "H3F3A" "APOBEC3A" "MT-CO3" "MYL6" "S100A9" "SOD2" "H1FX" "S100A8" "C1QA" "BIN2" "PLIN2"
## [1] ""
## [1] "FCER1A" "CLEC10A" "HLA-DPB1" "CD74" "HLA-DRA" "HLA-DRB1" "CST7" "RPLP1" "LMNA" "GSN" "IL32" "SPINT2" "CD7" "GNLY" "CCL5" "SDC2" "KLRB1" "GZMB" "NKG7" "SMOX" "PDLIM1" "FGFBP2" "TAGLN2" "DCTN2" "SPON2" "GZMA" "G0S2" "HOPX" "GAPDH" "FABP5"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "PPBP" "HIST1H2AC" "PF4" "SDPR" "NRGN" "GNG11" "CCL5" "TUBB1" "ACRBP" "CLU" "RGS18" "F13A1" "RUFY1" "MMD" "NGFRAP1" "MAX" "NCOA4" "VCL" "LIMS1" "TSC22D1" "TUBA4A" "VIM-AS1" "RNF11" "YWHAH" "MAP3K7CL" "CCND3" "TLN1" "XPNPEP1" "ETFA" "GRAP2"
## [1] ""
## [1] "RPL34" "RPLP1" "S100A6" "S100A4" "LYZ" "S100A9" "AIF1" "RPS19" "S100A8" "HLA-DRA" "MALAT1" "NEAT1" "RP11-1143G9.4" "S100A12" "HLA-DRB1" "CD74" "HLA-DPB1" "CSF3R" "OSM" "SNAPC1" "RAB34" "ERO1L" "NXT1" "FAM101B" "FABP5" "RETN" "HILPDA" "ELL" "FNDC3B" "KBTBD6"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "GPX1" "LYZ" "S100A9" "S100A8" "S100A12" "RP11-1143G9.4" "MIR4435-1HG" "SMOX" "CD9" "GAPDH" "SDPR" "RGS18" "GNG11" "PF4" "TUBB1" "MPP1" "ACTN1" "MAP3K7CL" "NRGN" "ACRBP" "RPLP1" "TUBA1C" "HIST1H2AC" "PPBP" "APP" "C19orf59" "RNF11" "PLBD1" "CLU" "F13A1"
## [1] ""
## [1] "NKG7" "GNLY" "GZMA" "GZMB" "KLRB1" "FGFBP2" "CST7" "CD7" "HOPX" "SPON2" "PRF1" "CCL4" "IL32" "CMC1" "RPS19" "CCL5" "MALAT1" "B2M" "JAK1" "MT-CO2" "BIN2" "CD47" "NAP1L1" "LYPD2" "MT-CO1" "MT2A" "CCL3" "RAP1B" "C1QA" "CCND3"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "HLA-DPB1" "RPS19" "NAP1L1" "CD74" "HLA-DRB1" "HLA-DRA" "FTH1" "LYPD2" "C1QA" "AIF1" "VMO1" "SAT1" "MALAT1" "RAP1B" "FAM110A" "MT2A" "CLEC10A" "BIN2" "FCER1A" "TIMP1" "ACTB" "ICAM2" "SNAP23" "NDUFA6" "ARL6IP5" "CD47" "MYL6" "SPINT2" "CTSL" "SNN"
## [1] ""
## [1] "S100A8" "S100A9" "S100A12" "LYZ" "RP11-1143G9.4" "GPX1" "RPLP1" "GNLY" "S100A6" "HOPX" "GZMA" "GZMB" "KLRB1" "SPON2" "NKG7" "FGFBP2" "PRF1" "CD7" "CCL5" "IL32" "CSF3R" "CST7" "CCL4" "MT-CO3" "RETN" "PPBP" "RPL34" "S100P" "IL8" "CYP1B1"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "FTL" "FTH1" "SAT1" "B2M" "AIF1" "TMSB4X" "PLIN2" "S100A4" "MALAT1" "H3F3B" "NEAT1" "SH3BGRL3" "OAZ1" "H1FX" "APOBEC3A" "ERO1L" "ACTB" "HK2" "NXT1" "HILPDA" "SRGN" "SOD2" "S100A6" "RGCC" "ADM" "C15orf48" "CTA-29F11.1" "SNAPC1" "ANKRD37" "ITM2B"
## [1] ""
## [1] "FCER1A" "CLEC10A" "HLA-DPB1" "CD74" "GSN" "SPINT2" "RPLP1" "IL32" "DCTN2" "F13A1" "CCL5" "SDPR" "PDLIM1" "PPBP" "CST7" "HLA-DRB1" "CCND3" "PF4" "DAPP1" "YWHAH" "GNG11" "EGR1" "MMD" "GRAP2" "NCOA4" "TUBB1" "TMEM70" "MLH3" "HIST1H2AC" "TAGLN2"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "HLA-DRA" "HLA-DRB1" "CD74" "FCER1A" "HLA-DPB1" "CLEC10A" "GAPDH" "LYZ" "CTA-29F11.1" "HILPDA" "GSN" "NXT1" "SPINT2" "ERO1L" "C15orf48" "PLIN2" "RGCC" "H3F3B" "HK2" "MAP3K8" "SNAPC1" "ANKRD37" "FABP5" "TPM4" "ADM" "SRGN" "HSPA5" "TAGLN2" "CST7" "RPLP1"
## [1] ""
## [1] "FTL" "LYPD2" "MT-CO2" "RPS19" "NEAT1" "S100A6" "NAP1L1" "S100A4" "AIF1" "C1QA" "SAT1" "RAP1B" "FAM110A" "MT-CO1" "RABGAP1L" "PPBP" "VMO1" "MT2A" "EGR1" "PF4" "MARCH2" "S100A12" "ARRB1" "LYL1" "GNG11" "ABTB1" "OAZ1" "MT-CO3" "TMEM91" "NRGN"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "SELPLG" "ALOX5AP" "GZMB" "CTSC" "CD68" "FCER1G" "SERPINF1" "CST3" "CLIC3" "IRF7" "VIMP" "TXN" "UGCG" "PTPRE" "PLD4" "S100A6" "NPC2" "IL3RA" "APP" "JKAMP" "CD4" "IGJ" "PPP1R14B" "TWF2" "TGFBI" "SLC38A2" "STMN1" "MS4A6A" "B2M" "AMICA1"
## [1] ""
## [1] "RPS27" "RPL18A" "RPL13A" "RPS27A" "RPL32" "RPL21" "RPL13" "RPS19" "RPL34" "RPS12" "RPL41" "CD52" "RPS29" "HLA-DRA" "CD69" "PTMA" "RPS15A" "LTB" "RPL10" "ID3" "RPS18" "TAGAP" "RP5-887A10.1" "AC079767.4" "NEIL1" "YBX3" "ZNF331" "RHOB" "IGLL5" "HLA-DRB1"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "CASP2" "IL32" "ITM2A" "PHTF2" "NUAK2" "SKAP1" "RABEP2" "MRPS2" "TMEM80" "MT2A" "ZNF83" "RAB6A" "COQ10B" "PTPN4" "SDR39U1" "FBXO3" "ANXA1" "IFI6" "DCP2" "STK4" "ITGB7" "PHF6" "AC016831.7" "CCDC130" "LMNA" "MECP2" "GNG2" "COPS8" "TRAPPC2" "EML4"
## [1] ""
## [1] "GZMB" "SERPINF1" "FCER1G" "CLIC3" "CST3" "IRF7" "NPC2" "UGCG" "VIMP" "APP" "PLD4" "PTPRE" "CD4" "IL3RA" "PPP1R14B" "ALOX5AP" "TXN" "MS4A6A" "AMICA1" "TGFBI" "FCER1A" "HIGD1A" "PTGDS" "CCDC50" "STMN1" "RNASE6" "IGJ" "RRBP1" "XBP1" "SAMHD1"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "TMSB10" "CD52" "TMSB4X" "ACTB" "ACTG1" "IGLL5" "MZB1" "LTB" "SUB1" "PPIB" "SDF2L1" "MT-CO2" "C19orf10" "ITGB1" "SEC11C" "IGJ" "B2M" "SSR3" "ANXA6" "HLA-C" "HLA-A" "MT-CO1" "CALR" "MT-CYB" "ITGB7" "DNPH1" "PDIA6" "MT-ND4" "TXN" "MRPS14"
## [1] ""
## [1] "MALAT1" "FTH1" "RPS27" "RPL21" "EIF1" "H3F3B" "RPL34" "PMAIP1" "RPS27A" "ZNF331" "RGS2" "SNX9" "RPL32" "TRAF4" "RPS29" "EEF1A1" "RGS1" "PTMA" "IDI1" "NEAT1" "LY9" "PIK3R1" "BBC3" "WSB1" "NR4A2" "RPS19" "PTGDS" "PIM3" "CD69" "H1FX"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "CD74" "HLA-DRA" "LTB" "HLA-DRB1" "TMSB4X" "CD52" "RPS27" "RPL41" "IL4R" "SNX10" "RNASE6" "ACTB" "TMSB10" "CD72" "PLD4" "RPL34" "ALOX5AP" "TMEM80" "CD4" "SELPLG" "RPL13A" "CELF2" "SCOC" "ZCCHC7" "AMICA1" "RPL21" "ELMO1" "FCER1A" "TGFBI" "SDAD1"
## [1] ""
## [1] "SDF2L1" "SEC11C" "PPIB" "C19orf10" "MZB1" "XBP1" "PDIA6" "SSR3" "IGJ" "SUB1" "NEAT1" "PTMA" "ZNF331" "LITAF" "NR4A2" "RGS2" "CALR" "DERL1" "FTH1" "RPLP1" "ITGB1" "H3F3B" "LY9" "IDI1" "RGS1" "EIF1" "BBC3" "SLC2A3" "CORO7" "RPS15A"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "RPLP1" "RPL13" "RPS12" "RPL32" "RPL10" "RPS18" "RPS19" "RPS15A" "EEF1A1" "MGAT4A" "IGJ" "EBPL" "RPL41" "USP22" "RPL21" "PTGDS" "PIK3R1" "SUMF2" "ITM2A" "PPP1CC" "MARK3" "GMCL1" "ACAP2" "SSR3" "SDF2L1" "PRKAG1" "MRPS10" "ITGB1BP1" "PPP1R14B" "ACAA1"
## [1] ""
## [1] "HLA-DRB1" "CD74" "FOS" "HLA-DRA" "LITAF" "H3F3B" "MALAT1" "MT-CO1" "HEXIM1" "MT-CO3" "RGS1" "PTMA" "CD69" "LYZ" "RGS2" "TTC14" "NEAT1" "IDI1" "FTH1" "HSPB1" "ZNF331" "EIF1" "MT-CO2" "MT-CYB" "CD2BP2" "MT-ND4" "NCOA3" "SAMHD1" "PRPF4B" "CD72"
## [1] ""
## [1] ""
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
## [1] "SELPLG" "GZMB" "ALOX5AP" "CTSC" "CD68" "FCER1G" "SERPINF1" "CST3" "CLIC3" "IRF7" "VIMP" "TXN" "UGCG" "PTPRE" "NPC2" "PLD4" "IL3RA" "S100A6" "APP" "CD4" "JKAMP" "PPP1R14B" "IGJ" "TGFBI" "TWF2" "SLC38A2" "STMN1" "MS4A6A" "AMICA1" "HIGD1A"
## [1] ""
## [1] "RPS27" "CD52" "RPL18A" "RPL13A" "RPL32" "RPS27A" "RPL21" "RPL13" "LTB" "RPS19" "RPL34" "RPS12" "RPL41" "RPS29" "HLA-DRA" "CD69" "RPS15A" "IGLL5" "RPL10" "CD72" "ID3" "RPS18" "RP5-887A10.1" "TAGAP" "AC079767.4" "PTMA" "NEIL1" "YBX3" "ANXA6" "RHOB"
## [1] ""
## [1] ""
## [1] "PC2"
## [1] "GZMB" "SERPINF1" "FCER1G" "CLIC3" "CST3" "IRF7" "NPC2" "UGCG" "VIMP" "APP" "PLD4" "PTPRE" "CD4" "IL3RA" "PPP1R14B" "ALOX5AP" "TXN" "MS4A6A" "AMICA1" "TGFBI" "FCER1A" "PTGDS" "HIGD1A" "CCDC50" "STMN1" "RNASE6" "IGJ" "RRBP1" "XBP1" "SAMHD1"
## [1] ""
## [1] "CD52" "CASP2" "IL32" "ITM2A" "PHTF2" "NUAK2" "RABEP2" "SKAP1" "TMEM80" "MRPS2" "MT2A" "ZNF83" "RAB6A" "COQ10B" "PTPN4" "SDR39U1" "FBXO3" "ANXA1" "IFI6" "ITGB7" "DCP2" "STK4" "PHF6" "AC016831.7" "TRAPPC2" "LMNA" "DNPH1" "COPS8" "CCDC130" "MECP2"
## [1] ""
## [1] ""
## [1] "PC3"
## [1] "RPS27" "RPL21" "RPL34" "MALAT1" "RPL32" "CD74" "RPS27A" "RPS29" "RPL13" "HLA-DRA" "LTB" "RPS19" "NPC2" "EEF1A1" "UGCG" "RNASE6" "SIDT1" "PTGDS" "RPL18A" "APP" "ALOX5AP" "RPL13A" "GZMB" "TRAF4" "APPL1" "CD68" "MGAT4A" "PLD4" "SFPQ" "H1FX"
## [1] ""
## [1] "MZB1" "SDF2L1" "C19orf10" "PPIB" "SEC11C" "SUB1" "SSR3" "IGJ" "ACTG1" "ITGB1" "CALR" "PDIA6" "MT-CO2" "XBP1" "HLA-A" "IGLL5" "DERL1" "HLA-C" "ITGB7" "MT-CO1" "MT-CYB" "MRPS14" "TXN" "S100A6" "MT-CO3" "MT-ND4" "B2M" "TMSB10" "LITAF" "CD2BP2"
## [1] ""
## [1] ""
## [1] "PC4"
## [1] "CD74" "HLA-DRB1" "HLA-DRA" "MALAT1" "FOS" "H3F3B" "MT-CO1" "LITAF" "TMSB4X" "PTMA" "HEXIM1" "MT-CO3" "TTC14" "LYZ" "MT-CO2" "FTH1" "EIF1" "ACTB" "ZNF331" "ZCCHC7" "SAMHD1" "MT-ND4" "CD72" "HSPB1" "MT-CYB" "NEAT1" "CD69" "RGS1" "RP11-1143G9.4" "NCOA3"
## [1] ""
## [1] "RPLP1" "RPS12" "RPL10" "RPS15A" "RPL32" "RPL13" "RPS18" "MGAT4A" "RPS19" "EEF1A1" "IGJ" "USP22" "SDF2L1" "PIK3R1" "SSR3" "PTGDS" "EBPL" "ITM2A" "RPL21" "GMCL1" "SUMF2" "RPS27A" "MARK3" "CORO7" "IRF4" "PDIA6" "XBP1" "IL32" "PPP1R14B" "ACAP2"
## [1] ""
## [1] ""
## [1] "PC5"
## [1] "MGAT4A" "IRF4" "VHL" "ADAM17" "NKG7" "GNB1" "CCDC14" "RICTOR" "PDIA6" "RAB11FIP1" "H2AFJ" "MT-ND2" "CCDC69" "THAP7" "RAP2C" "YIPF5" "TLE4" "SIDT1" "HPS4" "TRAF4" "STMN1" "H3F3B" "MT-CYB" "SDAD1" "MT-CO3" "DSTN" "TRAPPC2" "MT-CO1" "MT-ND4" "RPS27A"
## [1] ""
## [1] "HLA-DRA" "SELPLG" "IL3RA" "AMICA1" "MS4A6A" "CD68" "FCER1A" "CD4" "CTSC" "FCER1G" "SCOC" "HLA-DRB1" "TGFBI" "IRF7" "S100A6" "SAMHD1" "LST1" "TP53I13" "SMAP1" "MRPS2" "PRKAG1" "RAB22A" "TWF2" "ACTG1" "JKAMP" "ITGB1BP1" "PPIE" "TXN" "CD74" "DCP2"
## [1] ""
## [1] ""
df <- map(c("not regressed", "regressed"), function(regr) {
tsne_list %>%
map(regr) %>%
map("data") %>%
bind_rows(.id = "cell_type")
})
names(df) <- c("original", "regressed")
df <- bind_rows(df, .id = "is_regressed")
tsne_regressed <- df %>%
mutate(cell_type = factor(cell_type, cell_types)) %>%
ggplot(aes_string("tSNE_1", "tSNE_2", color = "ident")) +
geom_point(size = 0.6) +
facet_grid(is_regressed ~ cell_type) +
labs(x = "tSNE1", y = "tSNE2") +
scale_color_manual("", values = c("red2", "royalblue1")) +
theme_classic() +
guides(colour = guide_legend(override.aes = list(size = 4)))
tsne_regressed
ggsave(
filename = str_c("results/plots/", Sys.Date(), "_tsne_regressed.pdf"),
plot = tsne_regressed,
device = "pdf",
width = 12,
height = 7
)
saveRDS(tsne_regressed, file = "results/R_objects/tsne_regressed_gg.rds")
# Plot only CD4
tsne_regressed_cd4 <- df %>%
dplyr::filter(cell_type == "CD4 T") %>%
ggplot(aes(tSNE_1, tSNE_2, color = ident)) +
geom_point(size = 0.25) +
facet_grid(is_regressed ~ .) +
theme_classic2() +
labs(x = "tSNE1", y = "tSNE2") +
scale_color_manual("", values = c("red2", "royalblue1"))
saveRDS(tsne_regressed_cd4, file = "results/R_objects/tsne_regressed_cd4.rds")2 Supplementary figure
plot_list <- readRDS("results/R_objects/validation_plots.rds")
plot_list[[4]] <- tsne_regressed
tsne_regressed +
theme(legend.position = "none",
strip.background = element_rect(fill = NA))
plot_list <- map(plot_list, function(gg) {
gg +
theme(legend.position = "none",
strip.background = element_rect(fill = "white"))
})
metasign_valid_gg <- ggarrange(
plotlist = plot_list[1:3],
ncol = 1,
nrow = 3,
labels = "auto",
align = "v"
)
metasign_valid_gg2 <- ggarrange(
plotlist = list(metasign_valid_gg, plot_list[[4]]),
ncol = 1,
nrow = 2,
heights = c(0.75, 0.25),
labels = c("", "d")
)
ggsave(
filename = str_c("doc/figures/R/", date, "_validation_figure.pdf"),
plot = metasign_valid_gg2,
width = 19,
height = 27,
units = "cm"
)
metasign_valid_gg3 Session Info
sessionInfo()## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 readr_1.3.1 tidyr_0.8.3 tibble_2.1.1 tidyverse_1.2.1 ggridges_0.5.1 scales_1.0.0 ggplotify_0.0.3 VennDiagram_1.6.20 futile.logger_1.4.3 GOstats_2.48.0 graph_1.60.0 Category_2.48.1 ROCR_1.0-7 gplots_3.0.1.1 caret_6.0-82 lattice_0.20-38 plotROC_2.2.1 ggrepel_0.8.0 purrr_0.3.2 pheatmap_1.0.12 SC3_1.10.1 biomaRt_2.38.0 org.Hs.eg.db_3.7.0 ggpubr_0.2 magrittr_1.5 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.6.7 AnnotationFilter_1.6.0 GenomicFeatures_1.34.7 AnnotationDbi_1.44.0 Seurat_2.3.4 Matrix_1.2-17 cowplot_0.9.4 scran_1.10.2 scater_1.10.1 ggplot2_3.1.0 SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0 DelayedArray_0.8.0
## [43] BiocParallel_1.16.6 matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0 BiocStyle_2.10.0
##
## loaded via a namespace (and not attached):
## [1] rtracklayer_1.42.2 AnnotationForge_1.24.0 ModelMetrics_1.2.2 prabclus_2.2-7 R.methodsS3_1.7.1 pkgmaker_0.27 acepack_1.4.1 bit64_0.9-7 knitr_1.22 irlba_2.3.3 R.utils_2.8.0 data.table_1.12.0 rpart_4.1-13 RCurl_1.95-4.12 doParallel_1.0.14 generics_0.0.2 metap_1.1 snow_0.4-3 lambda.r_1.2.3 RSQLite_2.1.1 RANN_2.6.1 proxy_0.4-23 bit_1.1-14 xml2_1.2.0 lubridate_1.7.4 httpuv_1.5.0 assertthat_0.2.1 viridis_0.5.1 gower_0.2.0 xfun_0.5 hms_0.4.2 evaluate_0.13 promises_1.0.1 DEoptimR_1.0-8 progress_1.2.0 readxl_1.3.1 caTools_1.17.1.2 Rgraphviz_2.26.0 igraph_1.2.4 DBI_1.0.0 htmlwidgets_1.3 backports_1.1.3 bookdown_0.9 trimcluster_0.1-2.1 annotate_1.60.1 gbRd_0.4-11 withr_2.1.2
## [48] robustbase_0.93-4 checkmate_1.9.1 GenomicAlignments_1.18.1 prettyunits_1.0.2 mclust_5.4.3 cluster_2.0.7-1 ape_5.3 segmented_0.5-3.0 lazyeval_0.2.2 crayon_1.3.4 genefilter_1.64.0 hdf5r_1.0.1 labeling_0.3 edgeR_3.24.3 recipes_0.1.5 pkgconfig_2.0.2 nlme_3.1-137 vipor_0.4.5 ProtGenerics_1.14.0 nnet_7.3-12 rlang_0.3.3 diptest_0.75-7 registry_0.5-1 modelr_0.1.4 doSNOW_1.0.16 cellranger_1.1.0 lmtest_0.9-36 rngtools_1.3.1 Rhdf5lib_1.4.3 zoo_1.8-5 base64enc_0.1-3 beeswarm_0.2.3 png_0.1-7 viridisLite_0.3.0 bitops_1.0-6 R.oo_1.22.0 KernSmooth_2.23-15 Biostrings_2.50.2 blob_1.1.1 DelayedMatrixStats_1.4.0 doRNG_1.7.1 lars_1.2 gridGraphics_0.3-0 GSEABase_1.44.0 memoise_1.1.0 plyr_1.8.4 ica_1.0-2
## [95] bibtex_0.4.2 gdata_2.18.0 zlibbioc_1.28.0 compiler_3.5.1 lsei_1.2-0 RColorBrewer_1.1-2 rrcov_1.4-7 fitdistrplus_1.0-14 cli_1.1.0 Rsamtools_1.34.1 dtw_1.20-1 XVector_0.22.0 pbapply_1.4-0 formatR_1.6 htmlTable_1.13.1 Formula_1.2-3 MASS_7.3-51.3 tidyselect_0.2.5 stringi_1.4.3 yaml_2.2.0 locfit_1.5-9.1 latticeExtra_0.6-28 tools_3.5.1 rstudioapi_0.10 foreach_1.4.4 foreign_0.8-71 gridExtra_2.3 prodlim_2018.04.18 Rtsne_0.15 rvcheck_0.1.3 digest_0.6.18 BiocManager_1.30.4 lava_1.6.5 shiny_1.2.0 fpc_2.1-11.1 Rcpp_1.0.1 broom_0.5.1 SDMTools_1.1-221 later_0.8.0 WriteXLS_4.1.0 httr_1.4.0 npsurv_0.4-0 kernlab_0.9-27 Rdpack_0.10-1 colorspace_1.4-1 rvest_0.3.2 XML_3.98-1.19
## [142] reticulate_1.11.1 splines_3.5.1 RBGL_1.58.2 statmod_1.4.30 flexmix_2.3-15 xtable_1.8-3 futile.options_1.0.1 jsonlite_1.6 dynamicTreeCut_1.63-1 timeDate_3043.102 modeltools_0.2-22 ipred_0.9-8 R6_2.4.0 Hmisc_4.2-0 pillar_1.3.1 htmltools_0.3.6 mime_0.6 glue_1.3.1 BiocNeighbors_1.0.0 class_7.3-15 codetools_0.2-16 tsne_0.1-3 pcaPP_1.9-73 mvtnorm_1.0-10 mixtools_1.1.0 curl_3.3 ggbeeswarm_0.6.0 gtools_3.8.1 GO.db_3.7.0 survival_2.44-1.1 limma_3.38.3 rmarkdown_1.12 munsell_0.5.0 e1071_1.7-1 rhdf5_2.26.2 GenomeInfoDbData_1.2.0 iterators_1.0.10 HDF5Array_1.10.1 haven_2.1.0 reshape2_1.4.3 gtable_0.3.0